# Bayesian and Classical Machine Learning Methods: A Comparison for Tree Species Classification with LiDAR Waveform Signatures

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## Abstract

**:**

## 1. Introduction

## 2. Materials and Methods

#### 2.1. Study Site

#### 2.2. Data

#### 2.2.1. LiDAR Data

_{0}(m), the Northing of first return y

_{0}(m), the height of first return z

_{0}(m), the pulse direction vectors (dx (m), dy (m) and dz (m)), the outgoing pulse reference bin location (leading edge 50% point of the outgoing pulse) and first return reference bin location (leading edge 50% point of the first return).

#### 2.2.2. Reference Data

#### 2.3. Methods

#### 2.3.1. Waveform Decomposition

#### 2.3.2. Tree Segmentation

#### 2.3.3. Feature Extraction from Waveform Signatures

#### 2.3.4. Feature Selection

**X**over all trees. This measure has been shown to be a reliable criterion for quantifying the variable importance of uncorrelated predictors. However, the traditional permutation accuracy importance is prone to bring about potential bias for variable selection when predictors vary in scales or the number of categories [27]. Additionally, the RF is likely to divide the importance amongst the correlated predictors. Consequently, none of these predictors may be significant for the model. Actually, the permutation results of the RF approach reflect independence between

_{j}**Xj**and both

**Y**and the remaining predictor variables

**Z**(

**X**) instead of only the importance of

_{1},… X_{j−1}, X_{j+1},…, X_{p}**Xj**in predicting the response

**Y**. Thus, we introduced a variant of permutation importance of the RF algorithm, conditional importance, to mitigate possible bias and avoid the impact of correlated variables for the feature selection in this study.

**Xj**and

**Y**are independent given the correlation structure between

**X**and

_{j}**Z**inherent in the data set. Within the framework of the conditional permutation,

**X**is permuted only in a discretized permutation grid rather than the whole dataset. The grid is determined by the partitions derived from the model fitting or cut points of empirical correlations between

_{j}**X**and

_{j}**Z**[27]. In the implementation, variables

**Z**whose correlation with

**X**meets the condition 1 − p-value > 0.2 are used for conditioning. For each grid, the out of bag (OOB) error prediction accuracy is measured in one tree after permuting the values of

_{j}**X**. Similar to the permutation importance, the conditional importance of

_{j}**X**is the average prediction accuracy of all classification trees.

_{j}#### 2.3.5. Tree Species Classification

#### Random Forests and Conditional Inference Forests

**X**is present, we aggregate predictions of the n trees’ results using the new data. Suppose that the ensemble of trees is${\left\{{T}_{i}\right\}}_{1}^{n}$, for regression, p(

**X**) =$\frac{1}{n}\sum _{1}^{n}{T}_{i}\left(\mathit{X}\right)$; for classification, p(

**X**) = majority votes ${\left\{{T}_{i}\left(\mathit{X}\right)\right\}}_{1}^{n}$. Within every tree, the OOB error is calculated using the remaining data from the original data as the OOB dataset.

#### Bayesian Inference

**Y**follows a multinomial distribution with sample size N and parameter vector p. y

_{i}is one of s unordered categories, labeled by$\text{}k=\left\{1,\cdots ,s\right\}$. When s is 2, the softmax model reduces to the logistic regression model.

_{i}takes value from 1 to s according to the covariate information. For outcome k, the underlying linear propensity ${\mathbf{\lambda}}_{\mathit{k}}$is denoted as:

_{1}= 0.

_{0}, S

_{0}) roughly derived from data can be assigned to these unknown regression parameters. In this study, empirical priors for these parameters (b

_{0}) were derived from multinomial logistic regression with a large standard deviation S

_{0}= 4, which can be assumed as weak informative priors. According to the Bayes’ rule, the posterior distribution of β can be written as:

**y**). The field-measured data were split into training and testing data using a random selection procedure. To mitigate the impact of this random selection procedure and different proportions of testing data on the variability of accuracy, we tested different proportions of testing data ranging from 0.15 to 0.35 with the interval of 0.025 on the model accuracy. The corresponding remaining proportion of data were used as training data to build models.

## 3. Results

#### 3.1. Tree Segmentation

#### 3.2. Feature Extraction & Selection

_{at}, WD

_{cw-sd}, TI

_{cw-sd}, HOHE

_{acwh}, WGD

_{ah}, RVegT

_{acwh}, E

_{at-sd}, VegI

_{rw-sd}and NP

_{cw-sd}were used for subsequent Bayesian inference for the tree species classification. Here, the subscript represents the variables’ source and statistical features (mean, max and standard deviation). For example, WD

_{at}denotes the WD from AWF of one tree segment along the time bins (at); WD

_{cw-sd}denotes that standard deviation of WDs derived from individual composite waveforms (cw) of one tree segment; WD

_{rw-sd}denotes that standard deviation of WDs derived from individual raw waveforms (rw) of one tree segment. Detailed descriptions of these variables can be found in Table A1.

#### 3.3. Classification Results

## 4. Discussion

#### 4.1. Tree Segmentation

#### 4.2. Individual Trees’ Waveform Signatures

#### 4.3. Waveform Metrics and Feature Selection

#### 4.4. Tree Species Classification and Uncertainty

## 5. Conclusions

## Acknowledgments

## Author Contributions

## Conflicts of Interest

## Appendix A

Waveform Metrics | Definition (Within an Individual Tree Segments) |
---|---|

Individual raw waveforms | |

Area | The area of an individual tree crown segment |

NP_{rw-mean} | The average number of detected peaks for raw waveforms |

NP_{rw-sd} | Standard deviation of NP |

MaxP_{rw} | Maximum of NP |

WD_{rw-mean} | The average distance from waveform beginning to waveform ending using raw waveform |

WD_{rw-sd} | Standard deviation of WD_{mean} |

HOME_{rw-mean} | The average distance from height of median energy in waveforms to the ground |

HOME_{rw-sd} | Standard deviation of HOME_{mean} |

HTMR_{rw-mean} | The average ration between HOHE and WD |

HTMR_{rw-sd} | Standard deviation of HTMR |

HOHE_{rw-mean} | The average distance from height of half energy in waveforms to the ground |

HOHE_{rw-sd} | Standard deviation of HOHE |

HTHR_{rw-mean} | The average ration between HOHE and WD |

HTHR_{rw-sd} | Standard deviation of HTHR |

FS_{rw-mean} | The average vertical angle from waveform beginning to the first peak |

FS_{rw-sd} | Standard deviation of FS |

ROUGH_{rw-mean} | The average distance form waveform beginning to the first peak |

ROUGH_{rw-sd} | Standard deviation of ROUGH |

TE_{rw-mean} | The average total energy of raw waveforms |

ME_{rw-mean} | The average energy of each raw waveform |

MaxI_{rw-mean} | Average maximum intensity of all raw waveforms |

TI_{rw-mean} | The average integral of energy along height from waveform beginning to the ground |

VegI_{rw-mean} | The average integral of energy along height from waveform beginning to 3-m above ground |

RVegT_{rw-mean} | The average ratio between VegI and TI |

MaxI_{rw-sd} | Standard deviation of maximum intensity |

TI_{rw-sd} | Standard deviation of the integral of energy along height from waveform beginning to the ground |

VegI_{rw-sd} | Standard deviation of the integral of energy along height from waveform beginning to 3-m above ground |

RVegT_{rw-sd} | Standard deviation of the ratio between VegI and TI for all waveforms in the individual tree crown segment |

Accumulative waveform along the time bin | |

NP_{at} | The number of peaks in the time bin based accumulative waveform |

WD_{at} | The distance from waveform beginning to the ground in the time bin based accumulative waveform |

HOME_{at} | The distance from height of median energy to ground in the time bin based accumulative waveform |

HOHE_{at} | The distance from height of half energy to ground in the time bin based accumulative waveform |

HTMR_{at} | The ration between HOME_{at} and WD_{at} |

HTHR_{at} | The ration between HOHE_{at} and WD_{at} |

FS_{at} | The front slope angle of the time bin based accumulative waveform |

ROUGH_{at} | The average distance form waveform beginning to the first peak in the time bin based accumulative waveform |

E_{at-mean} | The average energy of the time bin based accumulative waveform |

E_{at-sd} | Standard deviation of energy of the time bin based accumulative waveform |

Accumulative waveform along the height | |

NP_{ah} | The number of peaks in the height based accumulative waveform |

WD_{ah} | The distance from waveform beginning to the ground in the height based accumulative waveform |

HOME_{ah} | The distance from height of median energy to ground in the height based accumulative waveform |

HOHE_{ah} | The distance from height of half energy to ground in the height based accumulative waveform |

HTMR_{ah} | The ration between HOME_{ah} and WD_{ah} |

HTHR_{ah} | The ration between HOHE_{ah} and WD_{ah} |

FS_{ah} | The front slope angle of the height based accumulative waveform |

ROUGH_{ah} | The average distance form waveform beginning to the first peak in the height based accumulative waveform |

E_{ah-mean} | The average energy of the height based accumulative waveform |

E_{ah-sd} | Standard deviation of energy of the height based accumulative waveform |

MaxI_{ah} | Maximum intensity in height based accumulative waveform |

WD_{ah} | The distance from waveform beginning to the ground in the height based accumulative waveform |

TI_{ah} | The integral of energy along height from waveform beginning to the ground |

VegI_{ah} | The integral of energy along height from waveform beginning to 3-m above ground |

RVegT_{ah} | The ratio between VegI_{ah} and TI_{ah} |

Point cloud | |

A1_{p-mean} | The average amplitude of detected first peak of all waveforms within an individual tree crown segment |

A1_{p-sd} | Standard deviation of the amplitude of detected first peak for all waveforms within an individual tree crown segment |

TB1_{p-mean} | The average time bin locations of detected first peak for all waveforms within an individual tree crown segment |

TB1_{p-sd} | Standard deviation of the time bin locations of detected first peak for all waveforms within an individual tree crown segment |

EW1_{p-mean} | The average echo width of detected first peak for all waveforms within an individual tree crown segment |

EW1_{p-sd} | Standard deviation of the echo width of detected first peak for all waveforms within an individual tree crown segment |

A2_{p-mean} | The average amplitude of detected second peak of all waveforms within an individual tree crown segment |

A2_{p-sd} | Standard deviation of the amplitude of detected second peak for all waveforms within an individual tree crown segment |

TB2_{p-mean} | The average time bin locations of detected second peak for all waveforms within an individual tree crown segment |

TB2_{p-sd} | Standard deviation of the time bin locations of detected second peak for all waveforms within an individual tree crown segment |

EW2_{p-mean} | The average echo width of detected second peak for all waveforms within an individual tree crown segment |

EW2_{p-sd} | Standard deviation of the echo width of detected second peak for all waveforms within an individual tree crown segment |

A_{p-mean} | The average amplitude of all detected peaks of waveforms within an individual tree crown segment |

TB_{p-mean} | The average time bin locations of all detected peaks for waveforms within an individual tree crown segment |

EW_{p-mean} | The average echo width of all detected peak for waveforms within an individual tree crown segment |

A_{p-sd} | Standard deviation of amplitude for all detected peaks for waveforms within an individual tree crown segment |

TB_{p-sd} | Standard deviation of time bin locations of all detected peaks for waveforms within an individual tree crown segment |

EW_{p-sd} | Standard deviation of echo width of all detected peak for waveforms within an individual tree crown segment |

Individual composite waveforms | |

NP_{cw-mean} | The average number of detected peaks for these composite waveforms |

NP_{cw-sd} | Standard deviation of NP for the composite waveforms |

MaxP_{cw} | Maximum of NP for the composite waveforms |

WD_{cw-mean} | The average distance from waveform beginning to the ground for the composite waveforms |

WDcw-sd | Standard deviation of WD for the composite waveforms |

HOME_{cw-mean} | The average distance from height of median energy in waveforms to the ground for the composite waveforms |

HOME_{cw-sd} | Standard deviation of HOME for the composite waveforms |

HTMR_{cw-mean} | The average ration between HOHE and WD for the composite waveforms |

HTMR_{cw-sd} | Standard deviation of HTMR for the composite waveforms |

HOHE_{cw-mean} | The average distance from height of half energy in waveforms to the ground for the composite waveforms |

HOHE_{cw-sd} | Standard deviation of HOHE for the composite waveforms |

HTHR_{cw-mean} | The average ration between HOHE and WD for the composite waveforms |

HTHR_{cw-sd} | Standard deviation of HTHR for the composite waveforms |

FS_{cw-mean} | The average vertical angle from waveform beginning to the first peak for the composite waveforms |

FS_{cw-sd} | Standard deviation of FS for the composite waveforms |

ROUGH_{cw-mean} | The average distance form waveform beginning to the first peak for the composite waveforms |

ROUGH_{cw-sd} | Standard deviation of ROUGH for the composite waveforms |

TE_{cw-mean} | The average total energy of composite waveforms |

ME_{cw-mean} | The average energy of each composite waveform |

Accumulative composite waveforms | |

NP_{acwh} | The number of peaks in the height based accumulative composite waveform |

WD_{acwh} | The distance from waveform beginning to waveform ending in the height based accumulative composite waveform |

HOME_{acwh} | The distance from height of median energy to ground in the height based accumulative composite waveform |

HOHE_{acwh} | The distance from height of half energy to ground in the time height based accumulative composite waveform |

HTMR_{acwh} | The ration between HOME_{acwh} and WD_{acwh} |

HTHR_{acwh} | The ration between HOHE_{acwh} and WD_{acwh} |

FS_{acwh} | The front slope angle of the height based accumulative composite waveforms |

ROUGH_{acwh} | The average distance form waveform beginning to the first peak in height based accumulative composite waveform |

ME_{acwh} | The average energy of the height based accumulative composite waveforms |

MaxA_{acwh} | Maximum amplitude of the height accumulative composite waveforms |

WGD_{acwh} | The distance from waveform beginning to the ground in the height based accumulative composite waveform |

TI_{acwh} | The integral of energy along height using the accumulative composite waveform |

VegI_{acwh} | The integral of energy along height using the accumulative composite waveform |

RVegT_{acwh} | The ratio between VegI_{acwh} and TI_{acwh} using accumulative composite waveforms |

MaxI_{cw-mean} | Average maximum intensity of composite waveforms |

TI_{cw-mean} | The average integral of energy along height from waveform beginning to the ground using composite waveforms |

VegI_{cw-mean} | The average integral of energy along height from waveform beginning to 3 m above ground using composite waveforms |

groI_{cw-mean} | The average integral of energy along height from 3 m above ground to ground using composite waveforms |

RVegT_{cw-mean} | The average ratio between VegI and TI using composite waveforms |

MaxI_{cw-sd} | Standard deviation of maximum intensity using composite waveforms |

TI_{cw-sd} | Standard deviation of the integral of energy along height from waveform beginning to the ground using composite waveforms |

VegI_{cw-sd} | Standard deviation of the integral of energy along height from waveform beginning to 3 m above ground using composite waveforms |

GroI_{cw-sd} | Standard deviation of the integral of energy along height from 3 m above ground to ground using composite waveforms |

RVegT_{cw-sd} | Standard deviation of the ratio between VegI and TI using composite waveforms |

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**Figure 1.**An overview of study area with filed-measured plots in the San Joaquin Experimental Range (SJER).

**Figure 2.**Flowchart for the tree species classification using waveform LiDAR data. CHM: Canopy Height Model. RF: Random forests. CF: Conditional inference forests.

**Figure 3.**An example of tree segmentation with three approaches including the TreeVaW, watershed and TreeVaW + watershed (TW) algorithms.

**Figure 4.**An example of waveform signals falling into the boundary of the gray pine, interior live oak and blue oak. (

**a**) Point clouds after the Gaussian decomposition for three tree species. (

**b**) Vertical distribution of waveform signals (intensity) along height. Blue, yellow and black lines are 95% confidence interval (CI) of intensity, median intensity and mean of intensity along height, respectively. (

**c**) Accumulative waveforms (AWF) using raw waveforms along the time bin (red line) and height (black line) and composite waveforms along the height. (

**d**) An example of waveform metrics such as the waveform distance (WD), the height of half energy (HOHE), the height of waveform beginning to the ground (WGD), crown integral (VegI), ground integral (GI) derived from raw AWF along the height (black).

**Figure 5.**Comparison of variable importance for Random forests (RF) and Conditional inference forests (CF) methods using combined variables.

**Figure 7.**Overall accuracies of classification using variables from different sources such as composite waveforms (Composite), raw waveforms (Raw), waveform-based point cloud (Decomposition) and all combined variables (Combined) with different proportions of testing data across three methods (Bayesian, Random forests (RF) and Conditional inference forests (CF)).

**Table 1.**Description of 17 field plots used for modeling building and calibration with the number of trees, mean diameter at the breast height (DBH, m), mean tree height (m) and mean crown diameter (m) over different tree species.

Plot ID | Number of Trees | Mean DBH | Mean Tree Height | Mean Crown Diameter | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|

Gray Pine | Blue Oak | Interior Live Oak | Shrubs | Gray Pine | Blue Oak | Interior Live Oak | Shrubs | Gray Pine | Blue Oak | Interior Live Oak | Shrubs | ||

1 | 12 | 0.45 | - | 0.16 | 0.07 | 13.95 | - | 6.10 | 2.85 | 8.70 | - | 5.95 | 4.62 |

2 | 13 | 0.38 | 0.39 | 0.29 | - | 16.23 | 7.77 | 4.77 | 3.10 | 7.00 | 7.23 | 5.50 | 7.30 |

3 | 16 | 0.45 | 0.35 | 0.49 | 0.28 | 14.20 | 7.60 | 7.68 | 3.70 | 10.75 | 6.81 | 8.92 | 6.55 |

4 | 8 | - | 0.50 | 0.20 | - | - | 8.43 | 5.36 | - | - | 9.12 | 4.75 | - |

5 | 7 | - | - | 0.38 | - | - | - | 7.60 | - | - | - | 9.95 | - |

6 | 10 | 0.67 | 0.31 | - | - | 18.20 | 7.55 | - | 2.97 | 13.75 | 6.85 | - | 4.51 |

7 | 9 | - | - | 0.35 | - | - | - | 6.77 | - | - | - | 8.67 | - |

8 | 12 | 0.14 | - | 0.39 | 0.04 | 7.27 | - | 9.10 | 2.28 | 3.82 | - | 9.96 | 4.40 |

9 | 11 | - | 0.33 | 0.21 | 0.14 | - | 8.60 | 4.88 | 3.50 | - | 7.22 | 6.20 | 5.17 |

10 | 15 | 0.54 | 0.22 | 0.24 | 0.06 | 17.90 | 9.10 | 6.83 | 2.35 | 13.10 | 4.45 | 7.22 | 3.46 |

11 | 7 | - | - | 0.78 | - | - | - | 9.20 | - | - | - | 14.05 | - |

12 | 10 | 0.45 | - | - | 0.06 | 7.70 | - | - | 2.13 | 9.35 | - | - | 2.58 |

13 | 7 | - | 0.66 | - | - | - | 11.50 | - | - | - | 17.15 | - | - |

14 | 7 | - | - | 0.34 | - | - | - | 5.74 | - | - | - | 7.08 | - |

15 | 17 | 0.82 | 0.38 | 0.18 | 0.05 | 26.50 | 10.90 | 4.92 | 3.82 | 9.75 | 8.10 | 4.73 | 2.82 |

16 | 10 | 0.58 | - | 0.52 | - | 17.85 | - | 6.43 | - | 11.55 | - | 6.56 | - |

17 | 10 | - | - | 0.27 | 0.07 | - | - | 6.33 | 1.22 | - | - | 4.51 | 1.33 |

Total | 181 |

Approaches | Function | Minimum Height (m) | Tolerance | Extent |
---|---|---|---|---|

TreeVaW | 0.804x + 3.67 | 4 | - | - |

Watershed | - | 3.5 | 1 | 2 |

TreeVaW + Watershed (TW) | 0.1x + 2.15 | 2.5 | - | - |

Acronym (Metrics) | Description |
---|---|

WD (waveform distance) | The distance from the waveform beginning to waveform ending. |

WGD (waveform distance from ground) | The distance from the waveform beginning to assumed ground location. |

HOHE (height of median energy) | The distance from waveform centroid to the assumed ground location. |

MEHR (median energy height ratio) | HOHE/WGD |

ROUGH (roughness of outermost canopy) | The distance from the waveform beginning to the first peak. |

HOHE (height of half total energy) | The distance from half energy location to waveform ending. |

HEHR (half energy height ratio) | HOHE/WD |

FS (front slope angle) | The angle from waveform beginning to the first peak which is assumed to be canopy returns. |

E (total return energy) | The total energy contained in the waveform from waveform beginning to ending. |

VegI (integral of the vegetation part) | The integral of vegetation part which is 3 m above the assumed ground location. |

GI (integral of the ground part) | The integral of ground part which is 3 m from the assumed ground location. |

RvegT (the ratio between the integral of vegetation and the additive integral of vegetation and ground parts) | VegI/(VegI + GI) |

Approaches | Tree Detection Rate (%) | False Detection Rate (%) | Over-Segmentation Rate (%) |
---|---|---|---|

TreeVaW | 82.87 | 17.13 | 6.07 |

Watershed | 92.82 | 7.18 | 15.58 |

TreeVaW + Watershed (TW) | 90.06 | 9.94 | 8.84 |

**Table 5.**Confusion matrix for vegetation classification using RF and CF methods with training data (OOB error) (testing proportion = 0.2).

Observed | Gray Pine (%) | Blue Oak (%) | Interior Live Oak (%) | Shrub (%) | |
---|---|---|---|---|---|

Predicted | |||||

RF | |||||

Gray Pine | 95 | 5 | 7 | 0 | |

Blue Oak | 0 | 45 | 10 | 6 | |

Interior Live Oak | 5 | 40 | 80 | 6 | |

Shrub | 0 | 10 | 3 | 88 | |

Overall accuracy | 80 | Kappa | 72 | ||

CF | |||||

Gray Pine | 94 | 0 | 20 | 0 | |

Blue Oak | 0 | 20 | 0 | 0 | |

Interior Live Oak | 6 | 80 | 67 | 0 | |

Shrub | 0 | 0 | 13 | 100 | |

Overall accuracy | 68 | Kappa | 54 |

**Table 6.**Confusion matrix for vegetation classification using RF and CF methods with test data (testing proportion = 0.2).

Observed | Gray Pine (%) | Blue Oak (%) | Interior Live Oak (%) | Shrub (%) | |
---|---|---|---|---|---|

Predicted | |||||

RF | |||||

Gray Pine | 94 | 0 | 13 | 0 | |

Blue Oak | 6 | 50 | 13 | 0 | |

Interior Live Oak | 0 | 50 | 60 | 0 | |

shrub | 0 | 0 | 13 | 100 | |

Overall accuracy | 73 | Kappa | 61 | ||

CF | |||||

Gray Pine | 95 | 5 | 10 | 0 | |

Blue Oak | 0 | 10 | 3 | 0 | |

Interior Live Oak | 5 | 80 | 83 | 13 | |

shrub | 0 | 5 | 3 | 88 | |

Overall accuracy | 74 | Kappa | 63 | ||

Bayesian | |||||

Gray Pine | 89 | 0 | 8 | 0 | |

Blue Oak | 6 | 27 | 8 | 10 | |

Interior Live Oak | 6 | 73 | 83 | 20 | |

shrub | 0 | 0 | 0 | 70 | |

Overall accuracy | 84 | Kappa | 78 |

© 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

## Share and Cite

**MDPI and ACS Style**

Zhou, T.; Popescu, S.C.; Lawing, A.M.; Eriksson, M.; Strimbu, B.M.; Bürkner, P.C. Bayesian and Classical Machine Learning Methods: A Comparison for Tree Species Classification with LiDAR Waveform Signatures. *Remote Sens.* **2018**, *10*, 39.
https://doi.org/10.3390/rs10010039

**AMA Style**

Zhou T, Popescu SC, Lawing AM, Eriksson M, Strimbu BM, Bürkner PC. Bayesian and Classical Machine Learning Methods: A Comparison for Tree Species Classification with LiDAR Waveform Signatures. *Remote Sensing*. 2018; 10(1):39.
https://doi.org/10.3390/rs10010039

**Chicago/Turabian Style**

Zhou, Tan, Sorin C. Popescu, A. Michelle Lawing, Marian Eriksson, Bogdan M. Strimbu, and Paul C. Bürkner. 2018. "Bayesian and Classical Machine Learning Methods: A Comparison for Tree Species Classification with LiDAR Waveform Signatures" *Remote Sensing* 10, no. 1: 39.
https://doi.org/10.3390/rs10010039